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Intermittent Low Pressure on Zones - Hunter Controller

I have a problem with zones/circuits intermittently operating with low output - say around 1/10 of normal. The same zone will run fine most of the time, but then I'll find that it only has partially turned on at other times. This is across most of the zones of my system and it is intermittent. Last night I turned on a zone and half way through a 50 minute cycle, the output had decreased to approx 1/10 of normal. I checked the pressure on the well (well only serves the irrigation system) and it was 50-55psi. I then checked voltage on each of the circuits inside the controller while in this fault mode. Many circuits measured at 5mV (which is the off voltage that I have measured) but many measured at 117mV or 325mV. The operating circuit measured at 27V which is the low voltage output from the transformer. According to Hunter troubleshooting, if you have voltage on any other circuit except for the operating circuit, you have a controller problem.

So should I replace the controller or are there other suggestions to troubleshoot the problem?

So your bet (Wet Boots) is that somewhere in my 45 values, there is an intermittently defect valve that needs to be located and fixed/replaced. And that the controller is not likely the problem... Correct? I'll start the detective work!

The small differences in voltages are not a big concern to me. Is your pump on a pressure switch or a relay? If its a pressure switch it could be reaching pressure and shutting off until it hits the kick back on pressure causing flow to drop off. How big is your yard that you have 45 valves?